sponge

Flow past a sponge, a porous cylindrical lattice (parameters in geom/README.md), simulated with Basilisk. The sponge geometry is an STL file converted to a Basilisk dump, which the solver cylinder/cylinder.c restores with -d. The solver also has analytic shapes (-S cylinder, -S sphere) used for validation.

real.stl: the scanned sponge, centred and scaled to unit diameter by stl/center.py.

Flow is from left to right, Reynolds number 2000 above and 4000 below, based on the sponge diameter and the inlet velocity, both 1. The four surfaces are levels of the Q criterion, Q = 0.2, 0.6, 1.8 and 3, from the most transparent grey to the opaque pink. The dark body is real.stl. See Render for the commands.

Files:

• geom/gen.py: sponge parameters (config.py) to ver.stl
• stl/center.py: center the STL, scale the diameter to 1, axis along z
• stl/size.py: print z extent of an STL
• dump/stl2dump.c: STL to Basilisk dump, -w z LEVEL Z0 Z1 adds walls at the sponge ends
• dump/dump2xdmf.c: dump to XDMF for ParaView
• cylinder/cylinder.c: solver, cylinder -h lists options
• cylinder/deploy/cylinder.c: preprocessed solver source, needs only mpicc
• geom/0pre.sh, geom/0run.sh: SLURM scripts used for production runs

Install

Requires MPI, GNU make, Python 3 with numpy and scipy.

wget -q http://basilisk.fr/basilisk/basilisk.tar.gz
tar zxf basilisk.tar.gz
cd basilisk/src
cp config.gcc config    # macOS: cp config.osx config
(MAKEFLAGS=-j`nproc`; make ast && make qcc)
mkdir -p "$HOME/.local/bin" && cp qcc "$HOME/.local/bin/"

The path to basilisk/src is compiled into qcc, do not move the directory after building.

(cd cylinder && make cylinder)
(cd dump && make stl2dump dump2xdmf)

On macOS use make cylinder QCCFLAGS=-D_DARWIN_C_SOURCE and make stl2dump dump2xdmf CC=gcc-15 (Homebrew gcc, for OpenMP).

Run

mkdir sponge0 && cd sponge0
cat > config.py <<'EOF'
NV = 20
NC = 30
AA = 0.25
BB = 0.5
LOOP_NO = 1
R_E = 1.2
NumBelix = 1
NumBelix2 = 0
EOF
PYTHONPATH=. python3 ../geom/gen.py
../stl/center.py -v ver.stl center.stl
set -- $(../stl/size.py center.stl)
../dump/stl2dump -v -o -w z 6 $1 $2 -- -5 -6.25 -6.25 12.5  4 7  4 center.stl basilisk.dump
mpiexec -n 4 ../cylinder/cylinder -v -F -r 100 -p 100 -e 200 -Z $2 \
        -f force.dat -d basilisk.dump -o h -b pp

stl2dump arguments: X0 Y0 Z0 L minlevel maxlevel npe file.stl out.dump. The mesh is fixed by stl2dump and does not change during the run: minlevel everywhere (with -o the last 10% of the domain in x is coarser), maxlevel at the sponge surface, LEVEL at the walls. The wake is resolved at minlevel. Production runs use levels 10 13, see geom/0pre.sh.

Output: force.dat (columns: step, t, dt, total force, pressure force, viscous force, three components each), h.N.xdmf2 full field (with -F), h.y.N.xdmf2 and h.z.N.xdmf2 slices for ParaView, h.N.dump restart files (restart with -d h.N.dump -i). Cell attributes in h.N.attr.raw: p, lambda2, Q, u (3), omega (3); the slices also have cs and phi after Q.

Render

Iso-surfaces of |omega| (or the Q criterion with qVALUE, lambda2 with lVALUE) from the full-field output (-F), extracted with amriso (pip install git+https://github.com/cselab/amriso) and rendered with ParaView. The sponge surface comes from the STL. -Z ZCUT drops cells with |z| > ZCUT, to hide the boundary layers on the end walls. -X XCUT and -Y YCUT keep the surface inside the refined wake box and upstream of the outlet coarsening; without them the coarse far field contributes large flat facets.

python3 ../tool/iso.py -Z 1.6 1 h.[0-9]*.xdmf2
pvpython ../tool/pvsurf.py 1 center.stl h.[0-9]*.xdmf2
ffmpeg -framerate 4 -pattern_type glob -i 'h.*.omega1.png' -pix_fmt yuv420p omega1.mp4

tool/iso.py writes h.N.omega1.xdmf2 triangle meshes colored by omega_z, tool/pvsurf.py writes h.N.omega1.png with a fixed camera and color range over all frames. The camera is set from the STL alone, so it is the same in every frame. -w WIDTH -H HEIGHT sets the image size and -z ZOOM how much is in view; -w 3840 -H 2160 -z 0.83 puts the whole wake in a 16:9 frame. -A AZ,EL turns the camera. tool/pvmulti.py draws several levels of one frame with their own opacity and color (c colored by omega_z, b pale blue, p pink, or R/G/B), for example two Q levels:

python3 ../tool/iso.py -Z 1.6 q1,q5 h.[0-9]*.xdmf2
pvpython ../tool/pvmulti.py center.stl q1:0.3:b,q5:1.0:p h.[0-9]*.xdmf2